Geany defaults the save-as dialog to either:
1. the project base directory if a project is open, or 2. the directory set in `Edit->preferences->General->Startup->Startup path` if its set, or 3. leaves it to the GTK dialog which uses the working directory when Geany was started, which suits the command line folks.
Not sure what you mean by "registered" file, Geany does not have such a concept, do you mean the last file saved?
If so it probably would be possible to add either a setting `Default to last save directory` in `Edit->Preferences->Files->Saving files` where there are already a bunch of file saving checkboxes and/or a button on the dialog to select that directory with one click since the dialog needs to be shown anyway to get the filename.
Just needs somebody to contribute it.